open(BUFF,"mayo_ov_control_genotypes_for_mayogc.tfam") or die "no kk\n";
open(BUFF1,"KK2") or die "no kk2\n";
$line =<BUFF1>;
chomp($line);
@array = split(" ",$line);
shift(@array);
shift(@array);
shift(@array);
shift(@array);
$i =0;
while(<BUFF>)
{
	chomp($_);
	@array2 = split(" ",$_);
	$snp1 =$i;
	$i++;
	$snp2 = $i;
	$i++;
	$hash{$array2[1]} = "$array[$snp1] $array[$snp2]";
	#print "test $array2[1] $array[$snp1] $array[$snp2]\n";
	#die;

}
open(BUFF,"fwdStrandResults_mayo_ov_control_genotypes_for_mayogc.tfam")  or die "no file2\n";
open(BUFF1,"KK1") or die "no kk1\n";
$line =<BUFF1>;
chomp($line);
@array = ();
@array = split(" ",$line);
shift(@array);
shift(@array);
shift(@array);
shift(@array);
$i =0;
while(<BUFF>)
{
        chomp($_);
        @array1 = split(" ",$_);
        $snp1 =$i;
	$i++;
        $snp2 = $i;
	$array[$snp1] =~ tr/ATGC/TACG/;
	$array[$snp2] =~ tr/ATGC/TACG/;
	$i++;
        if(exists($hash{$array1[1]}))
	{
		if($hash{$array1[1]} ne "$array[$snp1] $array[$snp2]")
		{
			print "$hash{$array1[1]} eq $array[$snp1] $array[$snp2]\n";
		}
	}
}

